def test_find_callable():
assert fa.find([
dict(label='pre 2016-01-01'),
dict(label='post 2016-01-02'),
],
label=lambda val: val.startswith('post ')) == dict(
label='post 2016-01-02')
def anatomical_warp_inputs(acquisitions, **kwargs):
anatomical = fa.find(acquisitions, label='anatomical_mdeft')
return dict(
native=anatomical.find_file('*.nii.gz'),
standard=D99.find_file('D99_template.nii.gz'),
warp_target=D99.find_file('D99_atlas_1.2a.nii.gz'),
)
def dtiinit_inputs(acquisitions, **kwargs):
diffusion = fa.find(acquisitions, label='DTI 2mm b1250 84dir(axial)')
return dict(
bvec=diffusion.find_file('*.bvec'),
bval=diffusion.find_file('*.bval'),
nifti=diffusion.find_file('*.nii.gz'),
)
def reactivity_inputs(acquisition_label, acquisitions, session, **kwargs):
functional = fa.find_required_input_source(acquisitions, label=acquisition_label)
# using plain find() here b/c this T1w might be missing
structural = fa.find(acquisitions, label='T1w 1mm')
if not structural:
assert session['_id'] in second_to_first_visit_id,\
'the only sessions that should be missing T1w are second visits. {} was missing a T1w'\
.format(session['_id'])
first_visit_session_id = second_to_first_visit_id[session['_id']]
first_visit_acquisitions = client.request(
'sessions/{}/acquisitions'.format(first_visit_session_id)).json()
structural = fa.find(first_visit_acquisitions, label='T1w 1mm')
assert structural, 'Session {} is missing a structural.'.format(session['_id'])
return dict(
functional=functional.find_file('*.nii.gz'),
structural=structural.find_file('*.nii.gz'),
)
def dtiinit_inputs(acquisitions, **kwargs):
diffusion = fa.find(acquisitions, label='Diffusion')
return dict(
bvec=diffusion.find_file('*1000.bvec'),
bval=diffusion.find_file('*1000.bval'),
dwi=diffusion.find_file('*1000.nii.gz'),
), dict(
# Here you can add any configuration. So for instance to add robust tensor, do:
# fitMethod='rt'
)
def afq_inputs(analyses, **kwargs):
dtiinit = fa.find(analyses, label=dtiinit_label)
return dict(dtiInit_Archive=dtiinit.find_file('dtiInit_*.zip'), )
def test_find():
assert fa.find([
dict(label='pre'),
dict(label='post'),
], label='post') == dict(label='post')
from scitran_client import ScitranClient
import scitran_client.flywheel_analyzer as fa
client = ScitranClient('https://flywheel.scitran.stanford.edu')
with fa.installed_client(client):
D99 = fa.find(client.request(
'sessions/588bd1ac449f9800159305c2/acquisitions').json(),
label='atlas')
def anatomical_warp_inputs(acquisitions, **kwargs):
anatomical = fa.find(acquisitions, label='anatomical_mdeft')
return dict(
native=anatomical.find_file('*.nii.gz'),
standard=D99.find_file('D99_template.nii.gz'),
warp_target=D99.find_file('D99_atlas_1.2a.nii.gz'),
)
if __name__ == '__main__':
with fa.installed_client(client):
fa.run([
fa.define_analysis('afni-brain-warp',
anatomical_warp_inputs,
label='anatomical warp'),
],
project=fa.find_project(label='showdes'),
max_workers=2)